A thorough understanding of the normal bacterial flora associated with shrimp larviculture systems contributes to probiotic screening and disease control.The bacterial community of the water column over a commercial Litopenaeus vannamei larval rearing run was characterized with both culture-dependent and culture-independent methods.A total of 27 phylotypes at the species level were isolated and identified based on 16 S rDNA sequence analysis.Denaturing gradient gel electrophoresis(DGGE) analysis of the V3–V5 region of 16 S rRNA genes showed a dynamic bacterial community with major changes occurred from stages zoea to mysis during the rearing run.The sequences retrieved were affiliated to four phyla,Proteobacteria,Actinobacteria,Bacteroidetes,and Firmicutes,with the family Rhodobacteraceae being the most frequently recovered one.Subsequently,13 representative strains conferred higher larval survival than the control when evaluated in the in-vivo experiments;in particular,three candidates,assigned to Phaeobacter sp.,Arthrobacter sp.,and Microbacterium sp.,significantly improved larval survival( P <0.05).Therefore,the healthy shrimp larviculture system harbored a diverse and favorable bacterial flora,which contribute to larval development and are of great importance in exploiting novel probiotics. A thorough understanding of the normal bacterial flora associated with shrimp larviculture systems contributes to probiotic screening and disease control. Bacterial community of the water column over a commercial Litopenaeus vannamei larval rearing run was characterized with both culture-dependent and culture-independent methods. A total of 27 phylotypes at the species level were isolated and identified based on 16 S rDNA sequence analysis. Denaturing gradient gel electrophoresis (DGGE) analysis of the V3-V5 region of 16 S rRNA genes showed a dynamic bacterial community with major changes occurred from stages zoea to mysis during the rearing run. The sequences «said that the sequences were compared to four phyla, Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes, with the family Rhodobacteraceae being the most frequently recovered one.Subsequently, 13 representative- as in in-in-vivo experiments; in particular, three candida tes, assigned to Phaeobacter sp., Arthrobacter sp., and Microbacterium sp., significantly improved larval survival (P <0.05). Therefore, the healthy shrimp larviculture system harbored a diverse and favorable bacterial flora, which contribute to larval development and are of great importance in exploiting novel probiotics.